R/selected.R
In thomasgaquiere/Maria: Simulate Different Forms of Logging on a Forest
Defines functions
selected
Documented in
selected
#'Selection of trees to log
#'
#'@param inventory Input inventory (see the inputs formats and metadata in the
#' \code{\link{vignette}}) (data.frame)
#'
#'@param topography Digital terrain model (DTM) of the inventoried plot (LiDAR
#' or SRTM) (\code{\link{DTMParacou}}) (RasterLayer)
#'
#'@param scenario Logging scenario: "RIL1", "RIL2broken", "RIL2", "RIL3",
#' "RIL3fuel", "RIL3fuelhollow" or "manual"(character) (see the
#' \code{\link{vignette}})
#'
#'@param fuel Fuel wood exploitation: no exploitation = "0", exploitation of
#' damage and unused part of logged trees for fuel = "1", exploitation of
#' hollow trees, damage and and unused part of the log for fuel = "2"
#'
#'@param diversification TPossibility to log other species in addition to the
#' main commercial species (species with a value of 2 for commercial in the
#' \code{\link{SpeciesCriteria}} table) (logical)
#'
#'@param specieslax Allow diversification if the stand is too poor to reach the
#' objective volume without diversification, = FALSE by default (logical)
#'
#'@param VO Objective volume for the entire area of the plot (numeric value)
#'
#'@param HVinit Harvestable volume in the plot for the chosen scenario
#' (\code{\link{SpeciesCriteria}}) (numeric value)
#'
#'@param objectivelax Allow exploitation in case of non-achievement of the
#' objective volume (if stand too poor), = FALSE by default (logical)
#'
#'@param advancedloggingparameters Other parameters of the logging simulator
#' \code{\link{loggingparameters}} (list) MainTrail (multiline)
#'
#'@return Input inventory with
#'- The trees selected for harvesting ("Selected")
#'- if the Minimum Felling Diameter (MinFD) of their species has been raised
#' ("Up")
#'- The cumulative harvestable volume of harvestable trees("VolumeCumSum").
#'- The probability of a tree being probed hollow ("ProbedHollowProba") and the
#' probed hollow trees ("ProbedHollow").
#'See the outputs metadata in the \code{\link{vignette}}
#'
#'2 sets of spatial points: (HollowTrees and EnergywoodTrees)
#'
#'@details This function allows the selection of trees to be exploited among the
#' exploitable trees. It also informs about the trees that were finally found
#' to be hollow during the probe. If fuel = 2, the hollow trees will be
#' harvested and are therefore included in the objective volume. If fuel = 0 or
#' 1, the hollow trees will not be exploited, so the function looks for other
#' trees to reach the objective volume (if possible).
#'
#' If the harvestable volume is higher than the objective volume, MinFD of the
#' 1st economic rank species is increased.
#' If this is not enough and if diversification is allowed, MinFD of 2nd
#' economic level species is increased. Then, the trees to be harvested are
#' chosen in decreasing order of volume, until the objective volume is reached.
#'
#' If the harvestable volume is lower than the objective volume,
#' diversification can be applied if it was not already applied ('specieslax')
#' (trees of all commercial ranks are selected in decreasing order of volume
#' until the objective volume is reached), or harvesting can continue despite
#' an unreached objective volume, or be abandoned ('objectivelax')
#'
#'@seealso \code{\link{Paracou6_2016}}, \code{\link{SpeciesCriteria}},
#' \code{\link{DTMParacou}}, \code{\link{loggingparameters}}
#'
#'@export
#'
#'@importFrom dplyr arrange desc ungroup rowwise mutate group_by select filter
#'@importFrom tibble add_column
#'@importFrom sp coordinates proj4string
#'@importFrom sf st_as_sf
#'@importFrom raster crs
#'
#'
#' @examples
#' data(Paracou6_2016)
#' data(DTMParacou)
#' data(PlotSlope)
#' data(HarvestablePolygons)
#' data(Maintrails)
#'
#' inventory <- addtreedim(inventorycheckformat(Paracou6_2016),
#' volumeparameters = ForestZoneVolumeParametersTable)
#'
#' inventory <- ONFGuyafortaxojoin(inventory, SpeciesCriteria)
#'
#' harvestableOutputs <- harvestable(inventory, topography = DTMParacou,
#' diversification = TRUE, specieslax = FALSE, plotslope = PlotSlope,
#' harvestablepolygons = HarvestablePolygons, maintrails = MainTrails,
#' advancedloggingparameters = loggingparameters())
#'
#' inventory <- harvestableOutputs$inventory
#' HVinit <- harvestableOutputs$HVinit
#'
#' selecInventory <- selected(inventory, topography = DTMParacou,
#' scenario = "manual", fuel = "2", diversification = TRUE,
#' VO = 125, HVinit = HVinit, specieslax = FALSE, objectivelax = TRUE,
#' advancedloggingparameters = loggingparameters())$inventory
#'
selected <- function(
inventory,
topography,
scenario,
fuel = NULL,
diversification = NULL,
VO, # objective volume for the entire surface of the plot
HVinit, # initial Harvestable Volume
specieslax = FALSE,
objectivelax = FALSE,
advancedloggingparameters = loggingparameters()
){
# Arguments check
if(!inherits(inventory, "data.frame"))
stop("Argument 'inventory' of the 'selected' function must be a data.frame")
if(!all(unlist(lapply(list(diversification, specieslax, objectivelax), inherits, "logical")))
&& !is.null(diversification))
stop("Arguments 'diversification', 'specieslax' and 'objectivelax'
of the 'selected' function must be logical")
# if (!any(scenario == "RIL1" | scenario == "RIL2broken"| scenario == "RIL2"| scenario == "RIL3"| scenario == "RIL3fuel"|
# scenario == "RIL3fuelhollow"| scenario == "manual"))
# stop("The 'scenario' argument of the 'selected' function must be 'RIL1', 'RIL2broken', 'RIL2', 'RIL3', 'RIL3fuel', 'RIL3fuelhollow' or 'manual'")
# if (!any(fuel == "0" | fuel == "1"| fuel == "2" | is.null(fuel)))
# stop("The 'fuel' argument of the 'selected' function must be '0', '1', or '2'")
if(!inherits(advancedloggingparameters, "list"))
stop("Argument 'advancedloggingparameters' of the 'selected' function must be a list")
if(scenario == "manual" &&
(is.null(fuel) || is.null(diversification)))
stop("If you choose the 'manual' mode,
you must fill in the arguments 'fuel' and 'diversification'")
if(!all(unlist(lapply(list(VO, HVinit), inherits, "numeric"))))
stop("Arguments 'VO' and 'HVinit' of the 'selected' function must be numeric")
# Redefinition of the parameters according to the chosen scenario
scenariosparameters <- scenariosparameters(scenario = scenario,
fuel = fuel, diversification = diversification)
fuel <- scenariosparameters$fuel
diversification <- scenariosparameters$diversification
# Global variables
Accessible <- Circ <- CircCorr <- CodeAlive <- Commercial <- NULL
Commercial.genus <- Commercial.species <- Condition <- DBH <- NULL
DeathCause <- DistCrit <- Family <- ONFName <- Crumbs <- NULL
ForestZoneVolumeParametersTable <- Genus <- Logged <- NULL
TimberLoggedVolume <- LoggingStatus <- MaxFD <- MaxFD.genus <- NULL
MaxFD.species <- MinFD <- MinFD.genus <- MinFD.species <- NULL
NoHollowTimberLoggedVolume <- ParamCrownDiameterAllometry <- PlotSlope <- NULL
PlotTopo <- ProbedHollow <- ProbedHollowProba <- ScientificName <- NULL
Selected <- Slope <- SlopeCrit <- Species <- Species.genus <- NULL
SpeciesCriteria <- Taxo <- Taxo.family <- Taxo.genus <- Taxo.species <- NULL
TreeFellingOrientationSuccess <- TreeHarvestableVolume <- NULL
TreeHeight <- TrunkHeight <- Up <- UpMinFD <- UpMinFD.genus <- NULL
UpMinFD.species <- VernName.genus <- VernName.genus.genus <- NULL
VernName.species <- VolumeCumSum <- Xutm <- Yutm <- aCoef <- NULL
alpha <- alpha.family <- alpha.genus <- alpha.species <- bCoef <- NULL
beta.family <- beta.genus <- beta.species <- geometry <- idTree <- NULL
# Apply S. Schmitt's "Rotten" predictive model to identify probed hollow trees.
inventory <- inventory %>%
# Estimates the probability of being probed hollow
mutate(ProbedHollowProba = ifelse(LoggingStatus == "harvestable" | LoggingStatus == "harvestable2nd",
advancedloggingparameters$RottenModel(DBH), NA)) %>%
# generate either "1" or "0" randomly for each line, depending on the proba associated with the line:
rowwise() %>%
mutate(ProbedHollow = ifelse(!is.na(ProbedHollowProba),
sample(c(1,0), size = 1, replace = F, # 1 = hollow tree, 0 = not hollow
prob = c(ProbedHollowProba, 1-ProbedHollowProba)), NA)) %>%
mutate(ProbedHollow = factor(as.numeric(ProbedHollow)))
if(fuel != "2"){
HollowTable <- filter(inventory, ProbedHollow == "1"| is.na(ProbedHollow))
inventory <- filter(inventory, ProbedHollow == "0") # we continue with just healthy trees in fuel != "2" case
}
# if objective achieved at the first attempt
inventory <- inventory %>%
mutate(Selected = ifelse(HVinit == VO & LoggingStatus == "harvestable",
"1", NA))# if we have our volume, harvestable sp = selected sp
# Create a column to indicate Which sp is FD uped. "0" = no uped, "1"= uped
inventory <- add_column(inventory, Up = "0")
if (HVinit < VO){ #diversification is necessary, designate the secondary-economic-rank species too
if (!diversification && specieslax){
inventory <- inventory %>%
mutate(Condition = ifelse(LoggingStatus == "harvestable2nd"|LoggingStatus == "harvestable",TRUE, FALSE)) %>%
group_by(Condition) %>%
arrange(desc(TreeHarvestableVolume)) %>%
mutate(VolumeCumSum = cumsum(TreeHarvestableVolume)) %>%
ungroup() %>%
mutate(Selected = ifelse(Condition & VolumeCumSum <= VO, "1", NA)) %>%
select(-Condition, -VolumeCumSum)
HarvestableTable <- inventory %>%
filter(Selected == "1")
HVlax <- sum(HarvestableTable$TreeHarvestableVolume) # Harvestable volume, with specieslax permission
if (HVlax < VO && objectivelax)
message("The exploitable volume (= ",paste(round(HVlax, digits = 1)),"m^3) is still lower
(by ",paste(round(VO- HVlax, digits = 1)),"m^3) than your objective volume
despite the diversification
(without the diversification HVinit= ",paste(round(HVinit, digits = 1)),"m^3).
You have chosen to continue harvesting with a volume lower than your objective in this case.")
if (HVlax < VO && !objectivelax)
stop("The harvestable volume = ",paste(round(HVlax, digits = 1)),"m^3)
is still lower (by ",paste(round(VO- HVlax, digits = 1)),"m^3)
than your objective volume despite the diversification
(without the diversification HVinit= ",paste(round(HVinit, digits = 1)),"m^3).
By default or because of your choice, the simulation stops.
If you wish to continue the exploitation with of an exploitable volume lower
than your objective volume, you can use the argument 'objectivelax'.")
if (!HVlax == VO)
message("The harvestable volume (= ",paste(round(HVinit, digits = 1)),"m^3) was lower
(by ",paste(round(VO- HVinit, digits = 1)),"m^3) than your objective volume.
You have chosen to diversify your species selection in this case.
The exploitation was therefore carried out on this diversified selection of species.")
} else {
inventory <- inventory %>%
mutate(Condition = ifelse(LoggingStatus == "harvestable",TRUE, FALSE)) %>%
group_by(Condition) %>%
arrange(desc(TreeHarvestableVolume)) %>%
mutate(VolumeCumSum = cumsum(TreeHarvestableVolume)) %>%
ungroup() %>%
mutate(Selected = ifelse(Condition & VolumeCumSum <= VO, "1", NA)) %>%
select(-Condition, -VolumeCumSum)
}
if (!diversification && !specieslax && objectivelax)
message("The harvestable volume (= ",paste(round(HVinit, digits = 1)),"m^3) was lower
(by ",paste(round(VO- HVinit, digits = 1)),"m^3) than your objective volume.
You have chosen to continue logging without diversifying in this case.")
if (diversification && objectivelax)
message("The harvestable volume (= ",paste(round(HVinit, digits = 1)),"m^3) was lower
(by ",paste(round(VO- HVinit, digits = 1)),"m^3) than your objective volume.
You have chosen to continue logging in this case.")
if ((!specieslax & !objectivelax) | (diversification && !objectivelax))
stop("The harvestable volume (= ",paste(round(HVinit, digits = 1)),"m^3) is lower
(by ",paste(round(VO- HVinit, digits = 1)),"m^3) than your objective volume.
By default or because of your choice, the simulation stops.
If you wish to continue the exploitation with of a harvestable volume lower
than your objective volume, you can use the argument 'objectivelax'
or the diversification of species (if not already done).")
}
if (HVinit > VO) {
inventory <- inventory %>%
mutate(LoggingStatus = ifelse(LoggingStatus == "harvestable" &
Commercial == "1" & (DBH >= UpMinFD & DBH <= MaxFD), #designate preferred individuals of first economic rank species, when the plot is species-rich.
"harvestableUp", LoggingStatus))
if (!diversification) {
HarvestableTable <- inventory %>%
filter(LoggingStatus == "harvestableUp")
HVupCommercial1 <- sum(HarvestableTable$TreeHarvestableVolume) #Compute the harvestable volume with upgraded FD individuals
if (HVupCommercial1 == VO){
inventory <- inventory %>%
mutate(Selected = ifelse(HVupCommercial1 == VO & LoggingStatus == "harvestableUp", "1", NA))# if harvestableUp individuals are sufficient to have our volume, harvestableUp ind = selected ind
message("As the harvestable volume (= ",paste(round(HVinit, digits = 1)),"m^3) was higher
(by ",paste(round(HVinit-VO, digits = 1)),"m^3) than the objective volume,
the Minimum Falling Diameter (MinFD) of 1st economic rank species were increased.
The objective volume has now been reached.")
}
if (HVupCommercial1 > VO){
# only individuals with DBH > FD are taken, but not all because their volumes > VO
inventory <- inventory %>%
mutate(Condition = ifelse(LoggingStatus == "harvestableUp", TRUE, FALSE)) %>%
group_by(Condition) %>%
arrange(desc(TreeHarvestableVolume)) %>%
mutate(VolumeCumSum = cumsum(TreeHarvestableVolume)) %>%
ungroup() %>%
mutate(Selected = ifelse(Condition & VolumeCumSum <= VO, "1", NA)) %>%
select(-Condition, -VolumeCumSum)
HarvestableTable <- inventory %>%
filter(Selected == "1")
HVupCommercial1adjust <- sum(HarvestableTable$TreeHarvestableVolume) #Harvestable volume, with "1" rank species and upgraded FD individuals only
message("The harvestable volume (= ",paste(round(HVupCommercial1, digits = 1)),"m^3) was higher
(by ",paste(round(HVupCommercial1-VO, digits = 1)),"m^3) than your objective volume
despite the increase in Minimum Falling Diameter (MinFD)
(Initial harvestable volume = ",paste(round(HVinit, digits = 1)),"m^3).
Trees were selected by decreasing order of volume
until the objective volume was reached.")
}
if (HVupCommercial1 < VO){
inventory <- inventory %>%
mutate(Condition = ifelse(LoggingStatus == "harvestableUp"|LoggingStatus == "harvestable",TRUE,FALSE)) %>%
group_by(Condition) %>%
arrange(desc(TreeHarvestableVolume)) %>%
mutate(VolumeCumSum = cumsum(TreeHarvestableVolume)) %>%
ungroup() %>%
mutate(Selected = ifelse(Condition & VolumeCumSum <= VO, "1", NA)) %>%
select(-Condition, -VolumeCumSum)
HarvestableTable <- inventory %>%
filter(Selected == "1")
HVupCommercial1adjust <- sum(HarvestableTable$TreeHarvestableVolume) #Harvestable volume, with "1" rank species and upgraded FD individuals
message("As the harvestable volume (= ",paste(round(HVinit, digits = 1)),"m^3)
was higher (by ",paste(round(HVinit-VO, digits = 1)),"m^3) than the objective volume,
the Minimum Falling Diameters (MinFD) of the 1st economic rank species were increased to UpMinFD.
Some trees with DBH lower than the UpMinFD were however selected
to ensure that the objective volume was reached.")
}
}
if (diversification) {
HarvestableTable <- inventory %>%
filter(LoggingStatus == "harvestableUp" | LoggingStatus == "harvestable") #the upgraded 1st rank and normal 2nd rank.
HVupCommercial1 <- sum(HarvestableTable$TreeHarvestableVolume) #173.334 m3
if (HVupCommercial1 == VO){
inventory <- inventory %>%
mutate(Selected = ifelse(LoggingStatus == "harvestableUp" | LoggingStatus == "harvestable",
"1", NA))# if we have our volume, harvestable ind = selected ind
message("As the harvestable volume (= ",paste(round(HVinit, digits = 1)),"m^3) was higher (by ",paste(round(HVinit-VO, digits = 1)),"m^3) than the objective volume, the Minimum Falling Diameter (MinFD) of the 1st economic rank species were increased. The objective volume has now been reached. It was not necessary to increase the MinFD of the other economic species")
}
if (HVupCommercial1 < VO){
inventory <- inventory %>%
mutate(Condition = ifelse(LoggingStatus == "harvestableUp"|LoggingStatus == "harvestable",TRUE,FALSE)) %>%
group_by(Condition) %>%
arrange(desc(TreeHarvestableVolume)) %>%
mutate(VolumeCumSum = cumsum(TreeHarvestableVolume)) %>%
ungroup() %>%
mutate(Selected = ifelse(Condition & VolumeCumSum <= VO, "1", NA)) %>%
select(-Condition, -VolumeCumSum)
HarvestableTable <- inventory %>%
filter(Selected == "1")
HVupCommercial1adjust <- sum(HarvestableTable$TreeHarvestableVolume) #49.69643 Harvestable volume, with "1" rank species and upgraded FD individuals, and 2nd rank no upgraded FD individuals
message("As the harvestable volume (= ",paste(round(HVinit, digits = 1)),"m^3)
was higher (by ",paste(round(HVinit-VO, digits = 1)),"m^3) than the objective volume,
the Minimum Falling Diameters (MinFD) of the 1st economic rank species were increased to UpMinFD.
Some trees with DBH lower than the UpMinFD were however selected to ensure that the objective
volume was reached. It was not necessary to raise the MinFDs of other economic species.")
}
if (HVupCommercial1 > VO){
inventory <- inventory %>%
mutate(LoggingStatus = ifelse(LoggingStatus == "harvestable" & Commercial == "2" & DBH >= UpMinFD & DBH <= MaxFD, #designate preferred individuals of 2nd economic rank species too, when the plot is species-rich.
"harvestableUp", LoggingStatus))
HarvestableTable <- inventory %>%
filter(LoggingStatus == "harvestableUp")
HVupCommercial12 <- sum(HarvestableTable$TreeHarvestableVolume) #271.2342 Harvestable volume, with upgraded FD individuals
if (HVupCommercial12 == VO){
inventory <- inventory %>%
mutate(Selected = ifelse(LoggingStatus == "harvestableUp",
"1", NA))# if we have our volume, harvestable ind = selected ind
}
if (HVupCommercial12 != VO){
inventory <- inventory %>%
mutate(Condition = ifelse(LoggingStatus == "harvestableUp"|LoggingStatus == "harvestable",TRUE,FALSE)) %>%
group_by(Condition) %>%
arrange(desc(TreeHarvestableVolume)) %>%
mutate(VolumeCumSum = cumsum(TreeHarvestableVolume)) %>%
ungroup() %>%
mutate(Selected = ifelse(Condition & VolumeCumSum <= VO, "1", NA)) %>%
select(-Condition, -VolumeCumSum)
HarvestableTable <- inventory %>%
filter(Selected == "1")
HVupCommercial12adjust <- sum(HarvestableTable$TreeHarvestableVolume) #Harvestable volume, with upgraded FD individuals
}
message("As the harvestable volume (= ",paste(round(HVinit, digits = 1)),"m^3)
was higher (by ",paste(round(HVinit-VO, digits = 1)),"m^3)
than the objective volume, it was necessary to increase the Minimum Falling Diameter (MinFD)
of all species. The objective volume has now been reached.")
}
}
}
# if at this step there are no selected trees
if(!any(inventory$Selected == "1") & any(inventory$ProbedHollow == "0")){
inventory <- inventory %>%
mutate(Condition = ifelse(LoggingStatus == "harvestable", TRUE, FALSE)) %>%
group_by(Condition) %>%
arrange(desc(TreeHarvestableVolume)) %>%
mutate(VolumeCumSum = cumsum(TreeHarvestableVolume)) %>%
ungroup() %>%
mutate(Selected = ifelse(Condition & VolumeCumSum <= VO, "1", NA)) %>%
select(-Condition, -VolumeCumSum)
}
# No NA in Selected colomn
inventory <-mutate(inventory, Selected = ifelse(is.na(Selected) , "0", Selected))
# Complete to reach the objective volume 'with crumbs'
HarvestableTable <- inventory %>%
filter(Selected == "1")
MissingVolume <- VO - sum(HarvestableTable$TreeHarvestableVolume)
min <- MissingVolume - 1
inventory <- inventory %>%
mutate(Crumbs = ifelse((LoggingStatus == "harvestableUp"|LoggingStatus == "harvestable") & Selected != "1" &
(TreeHarvestableVolume > min & TreeHarvestableVolume <= MissingVolume),
TRUE, FALSE)) %>%
group_by(Crumbs) %>%
arrange(desc(TreeHarvestableVolume))
if(any(inventory$Crumbs)){
inventory$Selected[1] <- "1" # the most important remaining volume able to reach the objective
}
inventory <- inventory %>%
ungroup() %>%
select(-Crumbs)
# Add the probed hollow trees removed until now in fuel != 2 case
if(fuel != "2"){
inventory <- bind_rows(inventory, HollowTable)
}
# No NA in Selected colomn
inventory <-mutate(inventory, Selected = ifelse(is.na(Selected) , "0", Selected))
# Upgraded MinFD species:
# to inform for each individual if its species have been FD upgraded
inventory <- inventory %>%
group_by(ONFName) %>%
mutate(Up = ifelse(any(LoggingStatus == "harvestableUp"), "1", Up)) %>%
ungroup()
# if there are "deselected" trees and not of 'selected = 1'
if (any(inventory$ProbedHollow == "1") & !any(inventory$Selected == "1")) # probed hollow trees and no selected trees
stop("No trees were selected because they were all probed hollow
(",paste(round(sum(as.numeric(inventory$ProbedHollow == "1"), na.rm = TRUE), digits = 1)),
" probed hollow trees). Your objective volume may be too low (the few trees selected were found to be
hollow).")
# Create a POINTS VECTOR with coordinates of the probed hollow trees:
if (any(inventory$ProbedHollow == "1", na.rm = TRUE)) {
HollowTreesPoints <- inventory %>%
filter(ProbedHollow == "1")
sp::coordinates(HollowTreesPoints) <- ~ Xutm + Yutm
sp::proj4string(HollowTreesPoints) <- raster::crs(topography)
HollowTreesPoints <- st_as_sf(as(HollowTreesPoints,"SpatialPoints"))
# OUTPUTS list
selectedOutputs <- list(inventory = inventory,
HollowTreesPoints = HollowTreesPoints,
EnergywoodTreesPoints = st_point(x = c(NA_real_, NA_real_))) # empty point
} else {
selectedOutputs <- list(inventory = inventory,
HollowTreesPoints = st_point(x = c(NA_real_, NA_real_)), # empty point
EnergywoodTreesPoints = st_point(x = c(NA_real_, NA_real_)))
}
if ((fuel == "2") & any(inventory$ProbedHollow == "1", na.rm = TRUE)) {
# Hollow trees = fuel wood:
inventory <- inventory %>%
mutate(DeathCause = ifelse(Selected == "1" & ProbedHollow == "1", "hollowfuel", NA))# replace "NA" par "DeathCause" in this code line in the ONF simulator
# Create a POINTS VECTOR with coordinates of the energywood trees:
EnergywoodTreesPoints <- HollowTreesPoints
# OUTPUTS list
selectedOutputs <- list(inventory = inventory,
HollowTreesPoints = HollowTreesPoints,
EnergywoodTreesPoints = EnergywoodTreesPoints)
}
return(selectedOutputs) # return the new inventory and the 2 points vectors (HollowTrees and EnergywoodTrees)
}
thomasgaquiere/Maria documentation built on Dec. 24, 2021, 1:20 a.m.
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Defines functions selected
Documented in selected
#'Selection of trees to log
#'
#'@param inventory Input inventory (see the inputs formats and metadata in the
#' \code{\link{vignette}}) (data.frame)
#'
#'@param topography Digital terrain model (DTM) of the inventoried plot (LiDAR
#' or SRTM) (\code{\link{DTMParacou}}) (RasterLayer)
#'
#'@param scenario Logging scenario: "RIL1", "RIL2broken", "RIL2", "RIL3",
#' "RIL3fuel", "RIL3fuelhollow" or "manual"(character) (see the
#' \code{\link{vignette}})
#'
#'@param fuel Fuel wood exploitation: no exploitation = "0", exploitation of
#' damage and unused part of logged trees for fuel = "1", exploitation of
#' hollow trees, damage and and unused part of the log for fuel = "2"
#'
#'@param diversification TPossibility to log other species in addition to the
#' main commercial species (species with a value of 2 for commercial in the
#' \code{\link{SpeciesCriteria}} table) (logical)
#'
#'@param specieslax Allow diversification if the stand is too poor to reach the
#' objective volume without diversification, = FALSE by default (logical)
#'
#'@param VO Objective volume for the entire area of the plot (numeric value)
#'
#'@param HVinit Harvestable volume in the plot for the chosen scenario
#' (\code{\link{SpeciesCriteria}}) (numeric value)
#'
#'@param objectivelax Allow exploitation in case of non-achievement of the
#' objective volume (if stand too poor), = FALSE by default (logical)
#'
#'@param advancedloggingparameters Other parameters of the logging simulator
#' \code{\link{loggingparameters}} (list) MainTrail (multiline)
#'
#'@return Input inventory with
#'- The trees selected for harvesting ("Selected")
#'- if the Minimum Felling Diameter (MinFD) of their species has been raised
#' ("Up")
#'- The cumulative harvestable volume of harvestable trees("VolumeCumSum").
#'- The probability of a tree being probed hollow ("ProbedHollowProba") and the
#' probed hollow trees ("ProbedHollow").
#'See the outputs metadata in the \code{\link{vignette}}
#'
#'2 sets of spatial points: (HollowTrees and EnergywoodTrees)
#'
#'@details This function allows the selection of trees to be exploited among the
#' exploitable trees. It also informs about the trees that were finally found
#' to be hollow during the probe. If fuel = 2, the hollow trees will be
#' harvested and are therefore included in the objective volume. If fuel = 0 or
#' 1, the hollow trees will not be exploited, so the function looks for other
#' trees to reach the objective volume (if possible).
#'
#' If the harvestable volume is higher than the objective volume, MinFD of the
#' 1st economic rank species is increased.
#' If this is not enough and if diversification is allowed, MinFD of 2nd
#' economic level species is increased. Then, the trees to be harvested are
#' chosen in decreasing order of volume, until the objective volume is reached.
#'
#' If the harvestable volume is lower than the objective volume,
#' diversification can be applied if it was not already applied ('specieslax')
#' (trees of all commercial ranks are selected in decreasing order of volume
#' until the objective volume is reached), or harvesting can continue despite
#' an unreached objective volume, or be abandoned ('objectivelax')
#'
#'@seealso \code{\link{Paracou6_2016}}, \code{\link{SpeciesCriteria}},
#' \code{\link{DTMParacou}}, \code{\link{loggingparameters}}
#'
#'@export
#'
#'@importFrom dplyr arrange desc ungroup rowwise mutate group_by select filter
#'@importFrom tibble add_column
#'@importFrom sp coordinates proj4string
#'@importFrom sf st_as_sf
#'@importFrom raster crs
#'
#'
#' @examples
#' data(Paracou6_2016)
#' data(DTMParacou)
#' data(PlotSlope)
#' data(HarvestablePolygons)
#' data(Maintrails)
#'
#' inventory <- addtreedim(inventorycheckformat(Paracou6_2016),
#' volumeparameters = ForestZoneVolumeParametersTable)
#'
#' inventory <- ONFGuyafortaxojoin(inventory, SpeciesCriteria)
#'
#' harvestableOutputs <- harvestable(inventory, topography = DTMParacou,
#' diversification = TRUE, specieslax = FALSE, plotslope = PlotSlope,
#' harvestablepolygons = HarvestablePolygons, maintrails = MainTrails,
#' advancedloggingparameters = loggingparameters())
#'
#' inventory <- harvestableOutputs$inventory
#' HVinit <- harvestableOutputs$HVinit
#'
#' selecInventory <- selected(inventory, topography = DTMParacou,
#' scenario = "manual", fuel = "2", diversification = TRUE,
#' VO = 125, HVinit = HVinit, specieslax = FALSE, objectivelax = TRUE,
#' advancedloggingparameters = loggingparameters())$inventory
#'
selected <- function(
inventory,
topography,
scenario,
fuel = NULL,
diversification = NULL,
VO, # objective volume for the entire surface of the plot
HVinit, # initial Harvestable Volume
specieslax = FALSE,
objectivelax = FALSE,
advancedloggingparameters = loggingparameters()
){
# Arguments check
if(!inherits(inventory, "data.frame"))
stop("Argument 'inventory' of the 'selected' function must be a data.frame")
if(!all(unlist(lapply(list(diversification, specieslax, objectivelax), inherits, "logical")))
&& !is.null(diversification))
stop("Arguments 'diversification', 'specieslax' and 'objectivelax'
of the 'selected' function must be logical")
# if (!any(scenario == "RIL1" | scenario == "RIL2broken"| scenario == "RIL2"| scenario == "RIL3"| scenario == "RIL3fuel"|
# scenario == "RIL3fuelhollow"| scenario == "manual"))
# stop("The 'scenario' argument of the 'selected' function must be 'RIL1', 'RIL2broken', 'RIL2', 'RIL3', 'RIL3fuel', 'RIL3fuelhollow' or 'manual'")
# if (!any(fuel == "0" | fuel == "1"| fuel == "2" | is.null(fuel)))
# stop("The 'fuel' argument of the 'selected' function must be '0', '1', or '2'")
if(!inherits(advancedloggingparameters, "list"))
stop("Argument 'advancedloggingparameters' of the 'selected' function must be a list")
if(scenario == "manual" &&
(is.null(fuel) || is.null(diversification)))
stop("If you choose the 'manual' mode,
you must fill in the arguments 'fuel' and 'diversification'")
if(!all(unlist(lapply(list(VO, HVinit), inherits, "numeric"))))
stop("Arguments 'VO' and 'HVinit' of the 'selected' function must be numeric")
# Redefinition of the parameters according to the chosen scenario
scenariosparameters <- scenariosparameters(scenario = scenario,
fuel = fuel, diversification = diversification)
fuel <- scenariosparameters$fuel
diversification <- scenariosparameters$diversification
# Global variables
Accessible <- Circ <- CircCorr <- CodeAlive <- Commercial <- NULL
Commercial.genus <- Commercial.species <- Condition <- DBH <- NULL
DeathCause <- DistCrit <- Family <- ONFName <- Crumbs <- NULL
ForestZoneVolumeParametersTable <- Genus <- Logged <- NULL
TimberLoggedVolume <- LoggingStatus <- MaxFD <- MaxFD.genus <- NULL
MaxFD.species <- MinFD <- MinFD.genus <- MinFD.species <- NULL
NoHollowTimberLoggedVolume <- ParamCrownDiameterAllometry <- PlotSlope <- NULL
PlotTopo <- ProbedHollow <- ProbedHollowProba <- ScientificName <- NULL
Selected <- Slope <- SlopeCrit <- Species <- Species.genus <- NULL
SpeciesCriteria <- Taxo <- Taxo.family <- Taxo.genus <- Taxo.species <- NULL
TreeFellingOrientationSuccess <- TreeHarvestableVolume <- NULL
TreeHeight <- TrunkHeight <- Up <- UpMinFD <- UpMinFD.genus <- NULL
UpMinFD.species <- VernName.genus <- VernName.genus.genus <- NULL
VernName.species <- VolumeCumSum <- Xutm <- Yutm <- aCoef <- NULL
alpha <- alpha.family <- alpha.genus <- alpha.species <- bCoef <- NULL
beta.family <- beta.genus <- beta.species <- geometry <- idTree <- NULL
# Apply S. Schmitt's "Rotten" predictive model to identify probed hollow trees.
inventory <- inventory %>%
# Estimates the probability of being probed hollow
mutate(ProbedHollowProba = ifelse(LoggingStatus == "harvestable" | LoggingStatus == "harvestable2nd",
advancedloggingparameters$RottenModel(DBH), NA)) %>%
# generate either "1" or "0" randomly for each line, depending on the proba associated with the line:
rowwise() %>%
mutate(ProbedHollow = ifelse(!is.na(ProbedHollowProba),
sample(c(1,0), size = 1, replace = F, # 1 = hollow tree, 0 = not hollow
prob = c(ProbedHollowProba, 1-ProbedHollowProba)), NA)) %>%
mutate(ProbedHollow = factor(as.numeric(ProbedHollow)))
if(fuel != "2"){
HollowTable <- filter(inventory, ProbedHollow == "1"| is.na(ProbedHollow))
inventory <- filter(inventory, ProbedHollow == "0") # we continue with just healthy trees in fuel != "2" case
}
# if objective achieved at the first attempt
inventory <- inventory %>%
mutate(Selected = ifelse(HVinit == VO & LoggingStatus == "harvestable",
"1", NA))# if we have our volume, harvestable sp = selected sp
# Create a column to indicate Which sp is FD uped. "0" = no uped, "1"= uped
inventory <- add_column(inventory, Up = "0")
if (HVinit < VO){ #diversification is necessary, designate the secondary-economic-rank species too
if (!diversification && specieslax){
inventory <- inventory %>%
mutate(Condition = ifelse(LoggingStatus == "harvestable2nd"|LoggingStatus == "harvestable",TRUE, FALSE)) %>%
group_by(Condition) %>%
arrange(desc(TreeHarvestableVolume)) %>%
mutate(VolumeCumSum = cumsum(TreeHarvestableVolume)) %>%
ungroup() %>%
mutate(Selected = ifelse(Condition & VolumeCumSum <= VO, "1", NA)) %>%
select(-Condition, -VolumeCumSum)
HarvestableTable <- inventory %>%
filter(Selected == "1")
HVlax <- sum(HarvestableTable$TreeHarvestableVolume) # Harvestable volume, with specieslax permission
if (HVlax < VO && objectivelax)
message("The exploitable volume (= ",paste(round(HVlax, digits = 1)),"m^3) is still lower
(by ",paste(round(VO- HVlax, digits = 1)),"m^3) than your objective volume
despite the diversification
(without the diversification HVinit= ",paste(round(HVinit, digits = 1)),"m^3).
You have chosen to continue harvesting with a volume lower than your objective in this case.")
if (HVlax < VO && !objectivelax)
stop("The harvestable volume = ",paste(round(HVlax, digits = 1)),"m^3)
is still lower (by ",paste(round(VO- HVlax, digits = 1)),"m^3)
than your objective volume despite the diversification
(without the diversification HVinit= ",paste(round(HVinit, digits = 1)),"m^3).
By default or because of your choice, the simulation stops.
If you wish to continue the exploitation with of an exploitable volume lower
than your objective volume, you can use the argument 'objectivelax'.")
if (!HVlax == VO)
message("The harvestable volume (= ",paste(round(HVinit, digits = 1)),"m^3) was lower
(by ",paste(round(VO- HVinit, digits = 1)),"m^3) than your objective volume.
You have chosen to diversify your species selection in this case.
The exploitation was therefore carried out on this diversified selection of species.")
} else {
inventory <- inventory %>%
mutate(Condition = ifelse(LoggingStatus == "harvestable",TRUE, FALSE)) %>%
group_by(Condition) %>%
arrange(desc(TreeHarvestableVolume)) %>%
mutate(VolumeCumSum = cumsum(TreeHarvestableVolume)) %>%
ungroup() %>%
mutate(Selected = ifelse(Condition & VolumeCumSum <= VO, "1", NA)) %>%
select(-Condition, -VolumeCumSum)
}
if (!diversification && !specieslax && objectivelax)
message("The harvestable volume (= ",paste(round(HVinit, digits = 1)),"m^3) was lower
(by ",paste(round(VO- HVinit, digits = 1)),"m^3) than your objective volume.
You have chosen to continue logging without diversifying in this case.")
if (diversification && objectivelax)
message("The harvestable volume (= ",paste(round(HVinit, digits = 1)),"m^3) was lower
(by ",paste(round(VO- HVinit, digits = 1)),"m^3) than your objective volume.
You have chosen to continue logging in this case.")
if ((!specieslax & !objectivelax) | (diversification && !objectivelax))
stop("The harvestable volume (= ",paste(round(HVinit, digits = 1)),"m^3) is lower
(by ",paste(round(VO- HVinit, digits = 1)),"m^3) than your objective volume.
By default or because of your choice, the simulation stops.
If you wish to continue the exploitation with of a harvestable volume lower
than your objective volume, you can use the argument 'objectivelax'
or the diversification of species (if not already done).")
}
if (HVinit > VO) {
inventory <- inventory %>%
mutate(LoggingStatus = ifelse(LoggingStatus == "harvestable" &
Commercial == "1" & (DBH >= UpMinFD & DBH <= MaxFD), #designate preferred individuals of first economic rank species, when the plot is species-rich.
"harvestableUp", LoggingStatus))
if (!diversification) {
HarvestableTable <- inventory %>%
filter(LoggingStatus == "harvestableUp")
HVupCommercial1 <- sum(HarvestableTable$TreeHarvestableVolume) #Compute the harvestable volume with upgraded FD individuals
if (HVupCommercial1 == VO){
inventory <- inventory %>%
mutate(Selected = ifelse(HVupCommercial1 == VO & LoggingStatus == "harvestableUp", "1", NA))# if harvestableUp individuals are sufficient to have our volume, harvestableUp ind = selected ind
message("As the harvestable volume (= ",paste(round(HVinit, digits = 1)),"m^3) was higher
(by ",paste(round(HVinit-VO, digits = 1)),"m^3) than the objective volume,
the Minimum Falling Diameter (MinFD) of 1st economic rank species were increased.
The objective volume has now been reached.")
}
if (HVupCommercial1 > VO){
# only individuals with DBH > FD are taken, but not all because their volumes > VO
inventory <- inventory %>%
mutate(Condition = ifelse(LoggingStatus == "harvestableUp", TRUE, FALSE)) %>%
group_by(Condition) %>%
arrange(desc(TreeHarvestableVolume)) %>%
mutate(VolumeCumSum = cumsum(TreeHarvestableVolume)) %>%
ungroup() %>%
mutate(Selected = ifelse(Condition & VolumeCumSum <= VO, "1", NA)) %>%
select(-Condition, -VolumeCumSum)
HarvestableTable <- inventory %>%
filter(Selected == "1")
HVupCommercial1adjust <- sum(HarvestableTable$TreeHarvestableVolume) #Harvestable volume, with "1" rank species and upgraded FD individuals only
message("The harvestable volume (= ",paste(round(HVupCommercial1, digits = 1)),"m^3) was higher
(by ",paste(round(HVupCommercial1-VO, digits = 1)),"m^3) than your objective volume
despite the increase in Minimum Falling Diameter (MinFD)
(Initial harvestable volume = ",paste(round(HVinit, digits = 1)),"m^3).
Trees were selected by decreasing order of volume
until the objective volume was reached.")
}
if (HVupCommercial1 < VO){
inventory <- inventory %>%
mutate(Condition = ifelse(LoggingStatus == "harvestableUp"|LoggingStatus == "harvestable",TRUE,FALSE)) %>%
group_by(Condition) %>%
arrange(desc(TreeHarvestableVolume)) %>%
mutate(VolumeCumSum = cumsum(TreeHarvestableVolume)) %>%
ungroup() %>%
mutate(Selected = ifelse(Condition & VolumeCumSum <= VO, "1", NA)) %>%
select(-Condition, -VolumeCumSum)
HarvestableTable <- inventory %>%
filter(Selected == "1")
HVupCommercial1adjust <- sum(HarvestableTable$TreeHarvestableVolume) #Harvestable volume, with "1" rank species and upgraded FD individuals
message("As the harvestable volume (= ",paste(round(HVinit, digits = 1)),"m^3)
was higher (by ",paste(round(HVinit-VO, digits = 1)),"m^3) than the objective volume,
the Minimum Falling Diameters (MinFD) of the 1st economic rank species were increased to UpMinFD.
Some trees with DBH lower than the UpMinFD were however selected
to ensure that the objective volume was reached.")
}
}
if (diversification) {
HarvestableTable <- inventory %>%
filter(LoggingStatus == "harvestableUp" | LoggingStatus == "harvestable") #the upgraded 1st rank and normal 2nd rank.
HVupCommercial1 <- sum(HarvestableTable$TreeHarvestableVolume) #173.334 m3
if (HVupCommercial1 == VO){
inventory <- inventory %>%
mutate(Selected = ifelse(LoggingStatus == "harvestableUp" | LoggingStatus == "harvestable",
"1", NA))# if we have our volume, harvestable ind = selected ind
message("As the harvestable volume (= ",paste(round(HVinit, digits = 1)),"m^3) was higher (by ",paste(round(HVinit-VO, digits = 1)),"m^3) than the objective volume, the Minimum Falling Diameter (MinFD) of the 1st economic rank species were increased. The objective volume has now been reached. It was not necessary to increase the MinFD of the other economic species")
}
if (HVupCommercial1 < VO){
inventory <- inventory %>%
mutate(Condition = ifelse(LoggingStatus == "harvestableUp"|LoggingStatus == "harvestable",TRUE,FALSE)) %>%
group_by(Condition) %>%
arrange(desc(TreeHarvestableVolume)) %>%
mutate(VolumeCumSum = cumsum(TreeHarvestableVolume)) %>%
ungroup() %>%
mutate(Selected = ifelse(Condition & VolumeCumSum <= VO, "1", NA)) %>%
select(-Condition, -VolumeCumSum)
HarvestableTable <- inventory %>%
filter(Selected == "1")
HVupCommercial1adjust <- sum(HarvestableTable$TreeHarvestableVolume) #49.69643 Harvestable volume, with "1" rank species and upgraded FD individuals, and 2nd rank no upgraded FD individuals
message("As the harvestable volume (= ",paste(round(HVinit, digits = 1)),"m^3)
was higher (by ",paste(round(HVinit-VO, digits = 1)),"m^3) than the objective volume,
the Minimum Falling Diameters (MinFD) of the 1st economic rank species were increased to UpMinFD.
Some trees with DBH lower than the UpMinFD were however selected to ensure that the objective
volume was reached. It was not necessary to raise the MinFDs of other economic species.")
}
if (HVupCommercial1 > VO){
inventory <- inventory %>%
mutate(LoggingStatus = ifelse(LoggingStatus == "harvestable" & Commercial == "2" & DBH >= UpMinFD & DBH <= MaxFD, #designate preferred individuals of 2nd economic rank species too, when the plot is species-rich.
"harvestableUp", LoggingStatus))
HarvestableTable <- inventory %>%
filter(LoggingStatus == "harvestableUp")
HVupCommercial12 <- sum(HarvestableTable$TreeHarvestableVolume) #271.2342 Harvestable volume, with upgraded FD individuals
if (HVupCommercial12 == VO){
inventory <- inventory %>%
mutate(Selected = ifelse(LoggingStatus == "harvestableUp",
"1", NA))# if we have our volume, harvestable ind = selected ind
}
if (HVupCommercial12 != VO){
inventory <- inventory %>%
mutate(Condition = ifelse(LoggingStatus == "harvestableUp"|LoggingStatus == "harvestable",TRUE,FALSE)) %>%
group_by(Condition) %>%
arrange(desc(TreeHarvestableVolume)) %>%
mutate(VolumeCumSum = cumsum(TreeHarvestableVolume)) %>%
ungroup() %>%
mutate(Selected = ifelse(Condition & VolumeCumSum <= VO, "1", NA)) %>%
select(-Condition, -VolumeCumSum)
HarvestableTable <- inventory %>%
filter(Selected == "1")
HVupCommercial12adjust <- sum(HarvestableTable$TreeHarvestableVolume) #Harvestable volume, with upgraded FD individuals
}
message("As the harvestable volume (= ",paste(round(HVinit, digits = 1)),"m^3)
was higher (by ",paste(round(HVinit-VO, digits = 1)),"m^3)
than the objective volume, it was necessary to increase the Minimum Falling Diameter (MinFD)
of all species. The objective volume has now been reached.")
}
}
}
# if at this step there are no selected trees
if(!any(inventory$Selected == "1") & any(inventory$ProbedHollow == "0")){
inventory <- inventory %>%
mutate(Condition = ifelse(LoggingStatus == "harvestable", TRUE, FALSE)) %>%
group_by(Condition) %>%
arrange(desc(TreeHarvestableVolume)) %>%
mutate(VolumeCumSum = cumsum(TreeHarvestableVolume)) %>%
ungroup() %>%
mutate(Selected = ifelse(Condition & VolumeCumSum <= VO, "1", NA)) %>%
select(-Condition, -VolumeCumSum)
}
# No NA in Selected colomn
inventory <-mutate(inventory, Selected = ifelse(is.na(Selected) , "0", Selected))
# Complete to reach the objective volume 'with crumbs'
HarvestableTable <- inventory %>%
filter(Selected == "1")
MissingVolume <- VO - sum(HarvestableTable$TreeHarvestableVolume)
min <- MissingVolume - 1
inventory <- inventory %>%
mutate(Crumbs = ifelse((LoggingStatus == "harvestableUp"|LoggingStatus == "harvestable") & Selected != "1" &
(TreeHarvestableVolume > min & TreeHarvestableVolume <= MissingVolume),
TRUE, FALSE)) %>%
group_by(Crumbs) %>%
arrange(desc(TreeHarvestableVolume))
if(any(inventory$Crumbs)){
inventory$Selected[1] <- "1" # the most important remaining volume able to reach the objective
}
inventory <- inventory %>%
ungroup() %>%
select(-Crumbs)
# Add the probed hollow trees removed until now in fuel != 2 case
if(fuel != "2"){
inventory <- bind_rows(inventory, HollowTable)
}
# No NA in Selected colomn
inventory <-mutate(inventory, Selected = ifelse(is.na(Selected) , "0", Selected))
# Upgraded MinFD species:
# to inform for each individual if its species have been FD upgraded
inventory <- inventory %>%
group_by(ONFName) %>%
mutate(Up = ifelse(any(LoggingStatus == "harvestableUp"), "1", Up)) %>%
ungroup()
# if there are "deselected" trees and not of 'selected = 1'
if (any(inventory$ProbedHollow == "1") & !any(inventory$Selected == "1")) # probed hollow trees and no selected trees
stop("No trees were selected because they were all probed hollow
(",paste(round(sum(as.numeric(inventory$ProbedHollow == "1"), na.rm = TRUE), digits = 1)),
" probed hollow trees). Your objective volume may be too low (the few trees selected were found to be
hollow).")
# Create a POINTS VECTOR with coordinates of the probed hollow trees:
if (any(inventory$ProbedHollow == "1", na.rm = TRUE)) {
HollowTreesPoints <- inventory %>%
filter(ProbedHollow == "1")
sp::coordinates(HollowTreesPoints) <- ~ Xutm + Yutm
sp::proj4string(HollowTreesPoints) <- raster::crs(topography)
HollowTreesPoints <- st_as_sf(as(HollowTreesPoints,"SpatialPoints"))
# OUTPUTS list
selectedOutputs <- list(inventory = inventory,
HollowTreesPoints = HollowTreesPoints,
EnergywoodTreesPoints = st_point(x = c(NA_real_, NA_real_))) # empty point
} else {
selectedOutputs <- list(inventory = inventory,
HollowTreesPoints = st_point(x = c(NA_real_, NA_real_)), # empty point
EnergywoodTreesPoints = st_point(x = c(NA_real_, NA_real_)))
}
if ((fuel == "2") & any(inventory$ProbedHollow == "1", na.rm = TRUE)) {
# Hollow trees = fuel wood:
inventory <- inventory %>%
mutate(DeathCause = ifelse(Selected == "1" & ProbedHollow == "1", "hollowfuel", NA))# replace "NA" par "DeathCause" in this code line in the ONF simulator
# Create a POINTS VECTOR with coordinates of the energywood trees:
EnergywoodTreesPoints <- HollowTreesPoints
# OUTPUTS list
selectedOutputs <- list(inventory = inventory,
HollowTreesPoints = HollowTreesPoints,
EnergywoodTreesPoints = EnergywoodTreesPoints)
}
return(selectedOutputs) # return the new inventory and the 2 points vectors (HollowTrees and EnergywoodTrees)
}
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